DOI: 10.1038/nmeth.3547. Predicting effects of noncoding variants with deep learning

Predicting effects of noncoding variants with deep learning–based sequence model

10.1038/nmeth.3547

Crossref journal-article

Springer Science and Business Media LLC

Nature Methods (297)

Bibliography

Zhou, J., & Troyanskaya, O. G. (2015). Predicting effects of noncoding variants with deep learningâbased sequence model. Nature Methods, 12(10), 931â934.

Authors 2

Jian Zhou (first)
Olga G Troyanskaya (additional)

References 26 Referenced 1,994

Leslie, R., O'Donnell, C.J. & Johnson, A.D. Bioinformatics 30, i185–i194 (2014). (10.1093/bioinformatics/btu273) / Bioinformatics by R Leslie (2014)
Ritchie, G.R., Dunham, I., Zeggini, E. & Flicek, P. Nat. Methods 11, 294–296 (2014). (10.1038/nmeth.2832) / Nat. Methods by GR Ritchie (2014)
Kircher, M. et al. Nat. Genet. 46, 310–315 (2014). (10.1038/ng.2892) / Nat. Genet. by M Kircher (2014)
Fu, Y. et al. Genome Biol. 15, 480 (2014). (10.1186/s13059-014-0480-5) / Genome Biol. by Y Fu (2014)
Lee, D. et al. Nat. Genet. 47, 955–961 (2015). (10.1038/ng.3331) / Nat. Genet. by D Lee (2015)
Slattery, M. et al. Trends Biochem. Sci. 39, 381–399 (2014). (10.1016/j.tibs.2014.07.002) / Trends Biochem. Sci. by M Slattery (2014)
Benveniste, D., Sonntag, H.J., Sanguinetti, G. & Sproul, D. Proc. Natl. Acad. Sci. USA 111, 13367–13372 (2014). (10.1073/pnas.1412081111) / Proc. Natl. Acad. Sci. USA by D Benveniste (2014)
Whitaker, J.W., Chen, Z. & Wang, W. Nat. Methods 12, 265–272 (2015). (10.1038/nmeth.3065) / Nat. Methods by JW Whitaker (2015)
ENCODE Project Consortium. Nature 489, 57–74 (2012). (10.1038/nature11247)
Kundaje, A. et al. Nature 518, 317–330 (2015). (10.1038/nature14248) / Nature by A Kundaje (2015)
Arvey, A., Agius, P., Noble, W.S. & Leslie, C. Genome Res. 22, 1723–1734 (2012). (10.1101/gr.127712.111) / Genome Res. by A Arvey (2012)
Ghandi, M., Lee, D., Mohammad-Noori, M. & Beer, M.A. PLoS Comput. Biol. 10, e1003711 (2014). (10.1371/journal.pcbi.1003711) / PLoS Comput. Biol. by M Ghandi (2014)
Neph, S. et al. Nature 489, 83–90 (2012). (10.1038/nature11212) / Nature by S Neph (2012)
Cowper-Sal·lari, R. et al. Nat. Genet. 44, 1191–1198 (2012). (10.1038/ng.2416) / Nat. Genet. by R Cowper-Sal·lari (2012)
De Gobbi, M. et al. Science 312, 1215–1217 (2006). (10.1126/science.1126431) / Science by M De Gobbi (2006)
Weedon, M.N. et al. Nat. Genet. 46, 61–64 (2014). (10.1038/ng.2826) / Nat. Genet. by MN Weedon (2014)
Stenson, P.D. et al. Hum. Genet. 133, 1–9 (2014). (10.1007/s00439-013-1358-4) / Hum. Genet. by PD Stenson (2014)
Welter, D. et al. Nucleic Acids Res. 42, D1001–D1006 (2014). (10.1093/nar/gkt1229) / Nucleic Acids Res. by D Welter (2014)
Abecasis, G.R. et al. Nature 491, 56–65 (2012). (10.1038/nature11632) / Nature by GR Abecasis (2012)
Koboldt, D.C. et al. Genome Res. 22, 568–576 (2012). (10.1101/gr.129684.111) / Genome Res. by DC Koboldt (2012)
McVicker, G. et al. Science 342, 747–749 (2013). (10.1126/science.1242429) / Science by G McVicker (2013)
Karolchik, D. et al. Nucleic Acids Res. 42, D764–D770 (2014). (10.1093/nar/gkt1168) / Nucleic Acids Res. by D Karolchik (2014)
Siepel, A. et al. Genome Res. 15, 1034–1050 (2005). (10.1101/gr.3715005) / Genome Res. by A Siepel (2005)
Pollard, K.S., Hubisz, M.J., Rosenbloom, K.R. & Siepel, A. Genome Res. 20, 110–121 (2010). (10.1101/gr.097857.109) / Genome Res. by KS Pollard (2010)
Cooper, G.M. et al. Genome Res. 15, 901–913 (2005). (10.1101/gr.3577405) / Genome Res. by GM Cooper (2005)
Davydov, E.V. et al. PLoS Comput. Biol. 6, e1001025 (2010). (10.1371/journal.pcbi.1001025) / PLoS Comput. Biol. by EV Davydov (2010)

Dates

Type	When
Created	10 years ago (Aug. 24, 2015, 11:20 a.m.)
Deposited	2 years, 3 months ago (May 18, 2023, 7:32 p.m.)
Indexed	5 hours, 28 minutes ago (Aug. 28, 2025, 8:50 a.m.)
Issued	10 years ago (Aug. 24, 2015)
Published	10 years ago (Aug. 24, 2015)
Published Online	10 years ago (Aug. 24, 2015)
Published Print	9 years, 10 months ago (Oct. 1, 2015)

Funders 0

None

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        8,
        28
      ]
    ],
    "date-time": "2025-08-28T12:50:41Z",
    "timestamp": 1756385441197
  },
  "reference-count": 26,
  "publisher": "Springer Science and Business Media LLC",
  "issue": "10",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2015,
            8,
            24
          ]
        ],
        "date-time": "2015-08-24T00:00:00Z",
        "timestamp": 1440374400000
      },
      "content-version": "tdm",
      "delay-in-days": 0,
      "URL": "http://www.springer.com/tdm"
    }
  ],
  "content-domain": {
    "domain": [
      "link.springer.com"
    ],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2015,
        10
      ]
    ]
  },
  "DOI": "10.1038/nmeth.3547",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2015,
        8,
        24
      ]
    ],
    "date-time": "2015-08-24T15:20:38Z",
    "timestamp": 1440429638000
  },
  "page": "931-934",
  "update-policy": "http://dx.doi.org/10.1007/springer_crossmark_policy",
  "source": "Crossref",
  "is-referenced-by-count": 1994,
  "title": "Predicting effects of noncoding variants with deep learning\u2013based sequence model",
  "prefix": "10.1038",
  "volume": "12",
  "author": [
    {
      "given": "Jian",
      "family": "Zhou",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "Olga G",
      "family": "Troyanskaya",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "297",
  "published-online": {
    "date-parts": [
      [
        2015,
        8,
        24
      ]
    ]
  },
  "reference": [
    {
      "key": "BFnmeth3547_CR1",
      "doi-asserted-by": "publisher",
      "first-page": "i185",
      "DOI": "10.1093/bioinformatics/btu273",
      "volume": "30",
      "author": "R Leslie",
      "year": "2014",
      "unstructured": "Leslie, R., O'Donnell, C.J. & Johnson, A.D. Bioinformatics 30, i185\u2013i194 (2014).",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "BFnmeth3547_CR2",
      "doi-asserted-by": "publisher",
      "first-page": "294",
      "DOI": "10.1038/nmeth.2832",
      "volume": "11",
      "author": "GR Ritchie",
      "year": "2014",
      "unstructured": "Ritchie, G.R., Dunham, I., Zeggini, E. & Flicek, P. Nat. Methods 11, 294\u2013296 (2014).",
      "journal-title": "Nat. Methods"
    },
    {
      "key": "BFnmeth3547_CR3",
      "doi-asserted-by": "publisher",
      "first-page": "310",
      "DOI": "10.1038/ng.2892",
      "volume": "46",
      "author": "M Kircher",
      "year": "2014",
      "unstructured": "Kircher, M. et al. Nat. Genet. 46, 310\u2013315 (2014).",
      "journal-title": "Nat. Genet."
    },
    {
      "key": "BFnmeth3547_CR4",
      "doi-asserted-by": "publisher",
      "first-page": "480",
      "DOI": "10.1186/s13059-014-0480-5",
      "volume": "15",
      "author": "Y Fu",
      "year": "2014",
      "unstructured": "Fu, Y. et al. Genome Biol. 15, 480 (2014).",
      "journal-title": "Genome Biol."
    },
    {
      "key": "BFnmeth3547_CR5",
      "doi-asserted-by": "publisher",
      "first-page": "955",
      "DOI": "10.1038/ng.3331",
      "volume": "47",
      "author": "D Lee",
      "year": "2015",
      "unstructured": "Lee, D. et al. Nat. Genet. 47, 955\u2013961 (2015).",
      "journal-title": "Nat. Genet."
    },
    {
      "key": "BFnmeth3547_CR6",
      "doi-asserted-by": "publisher",
      "first-page": "381",
      "DOI": "10.1016/j.tibs.2014.07.002",
      "volume": "39",
      "author": "M Slattery",
      "year": "2014",
      "unstructured": "Slattery, M. et al. Trends Biochem. Sci. 39, 381\u2013399 (2014).",
      "journal-title": "Trends Biochem. Sci."
    },
    {
      "key": "BFnmeth3547_CR7",
      "doi-asserted-by": "publisher",
      "first-page": "13367",
      "DOI": "10.1073/pnas.1412081111",
      "volume": "111",
      "author": "D Benveniste",
      "year": "2014",
      "unstructured": "Benveniste, D., Sonntag, H.J., Sanguinetti, G. & Sproul, D. Proc. Natl. Acad. Sci. USA 111, 13367\u201313372 (2014).",
      "journal-title": "Proc. Natl. Acad. Sci. USA"
    },
    {
      "key": "BFnmeth3547_CR8",
      "doi-asserted-by": "publisher",
      "first-page": "265",
      "DOI": "10.1038/nmeth.3065",
      "volume": "12",
      "author": "JW Whitaker",
      "year": "2015",
      "unstructured": "Whitaker, J.W., Chen, Z. & Wang, W. Nat. Methods 12, 265\u2013272 (2015).",
      "journal-title": "Nat. Methods"
    },
    {
      "key": "BFnmeth3547_CR9",
      "doi-asserted-by": "crossref",
      "unstructured": "ENCODE Project Consortium. Nature 489, 57\u201374 (2012).",
      "DOI": "10.1038/nature11247"
    },
    {
      "key": "BFnmeth3547_CR10",
      "doi-asserted-by": "publisher",
      "first-page": "317",
      "DOI": "10.1038/nature14248",
      "volume": "518",
      "author": "A Kundaje",
      "year": "2015",
      "unstructured": "Kundaje, A. et al. Nature 518, 317\u2013330 (2015).",
      "journal-title": "Nature"
    },
    {
      "key": "BFnmeth3547_CR11",
      "doi-asserted-by": "publisher",
      "first-page": "1723",
      "DOI": "10.1101/gr.127712.111",
      "volume": "22",
      "author": "A Arvey",
      "year": "2012",
      "unstructured": "Arvey, A., Agius, P., Noble, W.S. & Leslie, C. Genome Res. 22, 1723\u20131734 (2012).",
      "journal-title": "Genome Res."
    },
    {
      "key": "BFnmeth3547_CR12",
      "doi-asserted-by": "publisher",
      "first-page": "e1003711",
      "DOI": "10.1371/journal.pcbi.1003711",
      "volume": "10",
      "author": "M Ghandi",
      "year": "2014",
      "unstructured": "Ghandi, M., Lee, D., Mohammad-Noori, M. & Beer, M.A. PLoS Comput. Biol. 10, e1003711 (2014).",
      "journal-title": "PLoS Comput. Biol."
    },
    {
      "key": "BFnmeth3547_CR13",
      "doi-asserted-by": "publisher",
      "first-page": "83",
      "DOI": "10.1038/nature11212",
      "volume": "489",
      "author": "S Neph",
      "year": "2012",
      "unstructured": "Neph, S. et al. Nature 489, 83\u201390 (2012).",
      "journal-title": "Nature"
    },
    {
      "key": "BFnmeth3547_CR14",
      "doi-asserted-by": "publisher",
      "first-page": "1191",
      "DOI": "10.1038/ng.2416",
      "volume": "44",
      "author": "R Cowper-Sal\u00b7lari",
      "year": "2012",
      "unstructured": "Cowper-Sal\u00b7lari, R. et al. Nat. Genet. 44, 1191\u20131198 (2012).",
      "journal-title": "Nat. Genet."
    },
    {
      "key": "BFnmeth3547_CR15",
      "doi-asserted-by": "publisher",
      "first-page": "1215",
      "DOI": "10.1126/science.1126431",
      "volume": "312",
      "author": "M De Gobbi",
      "year": "2006",
      "unstructured": "De Gobbi, M. et al. Science 312, 1215\u20131217 (2006).",
      "journal-title": "Science"
    },
    {
      "key": "BFnmeth3547_CR16",
      "doi-asserted-by": "publisher",
      "first-page": "61",
      "DOI": "10.1038/ng.2826",
      "volume": "46",
      "author": "MN Weedon",
      "year": "2014",
      "unstructured": "Weedon, M.N. et al. Nat. Genet. 46, 61\u201364 (2014).",
      "journal-title": "Nat. Genet."
    },
    {
      "key": "BFnmeth3547_CR17",
      "doi-asserted-by": "publisher",
      "first-page": "1",
      "DOI": "10.1007/s00439-013-1358-4",
      "volume": "133",
      "author": "PD Stenson",
      "year": "2014",
      "unstructured": "Stenson, P.D. et al. Hum. Genet. 133, 1\u20139 (2014).",
      "journal-title": "Hum. Genet."
    },
    {
      "key": "BFnmeth3547_CR18",
      "doi-asserted-by": "publisher",
      "first-page": "D1001",
      "DOI": "10.1093/nar/gkt1229",
      "volume": "42",
      "author": "D Welter",
      "year": "2014",
      "unstructured": "Welter, D. et al. Nucleic Acids Res. 42, D1001\u2013D1006 (2014).",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "BFnmeth3547_CR19",
      "doi-asserted-by": "crossref",
      "first-page": "56",
      "DOI": "10.1038/nature11632",
      "volume": "491",
      "author": "GR Abecasis",
      "year": "2012",
      "unstructured": "Abecasis, G.R. et al. Nature 491, 56\u201365 (2012).",
      "journal-title": "Nature"
    },
    {
      "key": "BFnmeth3547_CR20",
      "doi-asserted-by": "publisher",
      "first-page": "568",
      "DOI": "10.1101/gr.129684.111",
      "volume": "22",
      "author": "DC Koboldt",
      "year": "2012",
      "unstructured": "Koboldt, D.C. et al. Genome Res. 22, 568\u2013576 (2012).",
      "journal-title": "Genome Res."
    },
    {
      "key": "BFnmeth3547_CR21",
      "doi-asserted-by": "publisher",
      "first-page": "747",
      "DOI": "10.1126/science.1242429",
      "volume": "342",
      "author": "G McVicker",
      "year": "2013",
      "unstructured": "McVicker, G. et al. Science 342, 747\u2013749 (2013).",
      "journal-title": "Science"
    },
    {
      "key": "BFnmeth3547_CR22",
      "doi-asserted-by": "publisher",
      "first-page": "D764",
      "DOI": "10.1093/nar/gkt1168",
      "volume": "42",
      "author": "D Karolchik",
      "year": "2014",
      "unstructured": "Karolchik, D. et al. Nucleic Acids Res. 42, D764\u2013D770 (2014).",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "BFnmeth3547_CR23",
      "doi-asserted-by": "publisher",
      "first-page": "1034",
      "DOI": "10.1101/gr.3715005",
      "volume": "15",
      "author": "A Siepel",
      "year": "2005",
      "unstructured": "Siepel, A. et al. Genome Res. 15, 1034\u20131050 (2005).",
      "journal-title": "Genome Res."
    },
    {
      "key": "BFnmeth3547_CR24",
      "doi-asserted-by": "publisher",
      "first-page": "110",
      "DOI": "10.1101/gr.097857.109",
      "volume": "20",
      "author": "KS Pollard",
      "year": "2010",
      "unstructured": "Pollard, K.S., Hubisz, M.J., Rosenbloom, K.R. & Siepel, A. Genome Res. 20, 110\u2013121 (2010).",
      "journal-title": "Genome Res."
    },
    {
      "key": "BFnmeth3547_CR25",
      "doi-asserted-by": "publisher",
      "first-page": "901",
      "DOI": "10.1101/gr.3577405",
      "volume": "15",
      "author": "GM Cooper",
      "year": "2005",
      "unstructured": "Cooper, G.M. et al. Genome Res. 15, 901\u2013913 (2005).",
      "journal-title": "Genome Res."
    },
    {
      "key": "BFnmeth3547_CR26",
      "doi-asserted-by": "publisher",
      "first-page": "e1001025",
      "DOI": "10.1371/journal.pcbi.1001025",
      "volume": "6",
      "author": "EV Davydov",
      "year": "2010",
      "unstructured": "Davydov, E.V. et al. PLoS Comput. Biol. 6, e1001025 (2010).",
      "journal-title": "PLoS Comput. Biol."
    }
  ],
  "container-title": "Nature Methods",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "http://www.nature.com/articles/nmeth.3547.pdf",
      "content-type": "application/pdf",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "http://www.nature.com/articles/nmeth.3547",
      "content-type": "text/html",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "http://www.nature.com/articles/nmeth.3547.pdf",
      "content-type": "application/pdf",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2023,
        5,
        18
      ]
    ],
    "date-time": "2023-05-18T23:32:31Z",
    "timestamp": 1684452751000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://www.nature.com/articles/nmeth.3547"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2015,
        8,
        24
      ]
    ]
  },
  "references-count": 26,
  "journal-issue": {
    "issue": "10",
    "published-print": {
      "date-parts": [
        [
          2015,
          10
        ]
      ]
    }
  },
  "alternative-id": [
    "BFnmeth3547"
  ],
  "URL": "http://dx.doi.org/10.1038/nmeth.3547",
  "relation": {},
  "ISSN": [
    "1548-7091",
    "1548-7105"
  ],
  "subject": [],
  "container-title-short": "Nat Methods",
  "published": {
    "date-parts": [
      [
        2015,
        8,
        24
      ]
    ]
  },
  "assertion": [
    {
      "value": "26 February 2015",
      "order": 1,
      "name": "received",
      "label": "Received",
      "group": {
        "name": "ArticleHistory",
        "label": "Article History"
      }
    },
    {
      "value": "11 June 2015",
      "order": 2,
      "name": "accepted",
      "label": "Accepted",
      "group": {
        "name": "ArticleHistory",
        "label": "Article History"
      }
    },
    {
      "value": "24 August 2015",
      "order": 3,
      "name": "first_online",
      "label": "First Online",
      "group": {
        "name": "ArticleHistory",
        "label": "Article History"
      }
    },
    {
      "value": "The authors declare no competing financial interests.",
      "order": 1,
      "name": "Ethics",
      "group": {
        "name": "EthicsHeading",
        "label": "Competing interests"
      }
    }
  ]
}